Re: [gmx-users] surrounding a peptide by ions of magnesium

2013-05-02 Thread Justin Lemkul
On 5/2/13 7:33 AM, Mohan maruthi sena wrote: Hi , Thanks for a quick reply. Sorry for not being clear, I want to surround the peptide with just ions(sodium). How can I do this? genbox -ci -nmol You will need a coordinate file for a single Mg2+ ion to be inserted, which is trivia

Re: [gmx-users] surrounding a peptide by ions of magnesium

2013-05-02 Thread Mohan maruthi sena
Hi , Thanks for a quick reply. Sorry for not being clear, I want to surround the peptide with just ions(sodium). How can I do this? Thanks, Mohan On Thu, May 2, 2013 at 4:58 PM, Justin Lemkul wrote: > > > On 5/2/13 12:38 AM, Mohan maruthi sena wrote: > >> Hi all, >> I hav

Re: [gmx-users] surrounding a peptide by ions of magnesium

2013-05-02 Thread Justin Lemkul
On 5/2/13 12:38 AM, Mohan maruthi sena wrote: Hi all, I have system consisting of a peptide(alpha-helix), I want the peptide to be surrounded by magnesium ions(instead of water). How can i do this gromacs? How can I find the concentration of magnesium ions. just like in solution we

[gmx-users] surrounding a peptide by ions of magnesium

2013-05-01 Thread Mohan maruthi sena
Hi all, I have system consisting of a peptide(alpha-helix), I want the peptide to be surrounded by magnesium ions(instead of water). How can i do this gromacs? How can I find the concentration of magnesium ions. just like in solution we have 0.5 Molar Mg+2 solution, My question how can